To perform the necessary electrostatics calculations,
a protein or any other molecular context
being analyzed with SZMAP must already
have all hydrogens explicitly represented
before it can be used. This may mean
you will have to use a program such as
reduce [Word-1999]
(available at [reduce]) or some other
system to add hydrogens to a protein.
The OpenEye SZMAP application manual
describes one way to do this.

Also, each atom must have partial charges
assigned—formal charges are insufficient.
The pch utility provided with
the OpenEye SZMAP application adds AmberFF94 charges to
standard amino-acid residues and AM1BCC charges to non-standard
residues. Otherwise, you can use OpenEye’s Quacpac TK or any
other procedure to add partial charges.

To calculate probe energies, we initialize
a OESzmapEngine with a molecular
context, test if the point of interest is clashing,
and if not, calculate the energies. In the example below,
the energies at each ligand atom coordinate
are returned in a OESzmapResults
object, which is accessed for specific values.
Alternatively, OECalcSzmapValue could
be used to get a single OEEnsemble
value directly.

In addition to energy calculations, the Szmap TK
can be used to generate 3D conformations of probe
molecules at calculated points, annotated
with OEComponent
energies for each conformation. In the example below,
individual atoms are also generated at calculation
points, each annotated with OEEnsemble
values.